Prodigal Son
by ItachiUzumaki98
Summary: Tony Stark has a son he doesn't even know exists. Naruto Uzumaki has always pushed himself to be better than his father. After the Hammer drone attack at the Stark Expo, Naruto gets his hands on one of the drones. Months later Shield knocks down his door with guns and an opportunity.
1. Prologue

Disclaimer: I Do Not Own Naruto or Avengers

* * *

 **Triskelion, Washington D.C**

"Director, we've located the Hammer Drone. It's in New York."

"Stark?"

Agent Coulson shook his head folding his hands behind his back. "We do not believe so, sir. Mr. Stark doesn't legally own the building."

"And illegally?"

"Unknown, sir," Coulson answered.

Standing from his chair, the Director of S.H.E.I.L.D, Nick Fury walked to the window overlooking D.C. From here he had a view of the city some would pay thousands for. He got if for free. All he had to do was protect the United States from threats, foreign and domestic. His job, to other, but he didn't see it as such. It was a responsibility to protect his home. To do that he needed to stay ten steps ahead, in intelligence, manpower, and technology. Right now he was behind in all of those but one.

SHIELD scientist lacked the intelligence to recreate Stark's Iron man armor, and without that technology, they couldn't combat terrorist like Ivan Vanko.

The Hammer drones were the only piece of Arc reactor technology not in Stark's hands. And given that Stark was keeping his cards close to his chest, this was the only chance that they would have to get something even close to that kind of tech.

"Take a team. Bring me that drone." He ordered his one good eye narrowing.

"Yes, sir." Coulson nodded and exited the room leaving the Director alone with his thoughts.

Every drone, Justin Hammer had put on display had been destroyed when Vanko forced them to self-destruct. All but one.

One out of thirty-two, and they had no clue on as to who had not only been able to stop the self-destruction but steal away a man-sized robot without anyone knowing. _And hide it in an American city._

Not only were the thieves smart, they were cocky, and that was a dangerous combination. Whoever was working on the drone needed to be stopped.

...

 **New York City**

"Let's move," Coulson ordered drawing his pistol as the men under his command held up assault rifles. All six of the barrels pointing at the townhouse across the street.  
"Signals coming from the basement. Prisoners are preferable, but shoot to kill at your own discretion."

Coulson led the team forward glad they blocked off the street before they came in. If civilians saw seven men in full tactical gear and carrying automatic weapons whoever was in that basement would be alerted by their screams.

"Rumlow, you're on point. Rolin's get the door."

Pressing his shoulder against the brick wall of the townhouse, with two men behind him and the rest of the team on the other side of the yellow painted door Coulson nodded as Rolin's kneeled burning through the door lock with the Mouse Hole.

One by one they filed into the small stairway.

"Light's on," Coulson ordered as the door closed behind them locking the team in the dark.

At the bottom of the steps was another door.

"Break it down."

"Yes, sir." Rolin's tucked the Mouse Hole away in his vest and moved to the side as another agent stepped forward holding a battering ram. Grabbing the right side nodded as Rumlow counted down.

"Three...two...one!"

The wooden door flew from its hinges and Coulson entered the basement behind Rumlow who was already yelling orders.

"SHIELD! Get down on your knees! On your knees!"

Clearing the room as the rest of the team entered Coulson stopped letting STRIKE do their job. He had his own job.

"Prisoner secured, sir."

"Coulson!" Fury barked over the radio.

Staring at the drone standing in the corner Coulson brought a hand up to his ear. "We've got it, sir. The drone is here and the prisoner is secured."

"Get off me, bastard!"

Turning around Coulson circled the workbench covered in tools so he could get eyes on the prisoner.

 _Crap._ Being held under Rumlow's knee was a small figure squirming as he tried to get free. To small a figure to be an adult.

"Sir, we've got a problem."

...

 _"Shit. Shit. Shit. Shit!_

Sitting in a white room Naruto bounced his leg underneath the table he was handcuffed to. It was the only thing in the room other than him, the chair he was sitting in and the one-way window where the black op spooks who had taken him were watching.

He couldn't see them but he knew they were there. And he knew they were making him wait as an intimidation tactic.

Not a very good one since he knew what was happening but it was still working. He was getting nervous.

Shield had got him red-handed with stolen tech and enough weaponry to take down a small country. Which wasn't really his fault. The drone had all the guns when he salvaged it.

 _"What was I supposed to do? Throw it away?"_ He couldn't just take a tank gun down the driveway and leave it on the curb. That was more dangerous than leaving it in his basement. Who knows what kind of people would have taken it.

Behind him, a door opened with an exaggerated creak. Another intimidation tactic.

"You're in a whole lot of trouble, kid."

Craning his neck Naruto looked over his shoulder as a tall black man with an eye patch and wearing a leather trench coat that went to his knees. He didn't look anything like what he assumed a government crony looked like. That weird smiling guy who arrested him looked like a government agent.

"My name is Nick Fury, I'm the director of the Strategic Homeland Intervention, Enforcement, and Logistics Division." Director Fury introduced circling the blonde child. "Naruto Uzumaki, age thirteen, born in New York City, 1997."

"Yes, sir." Naruto nodded.

Leaning over the table Director Fury set his hands down on the table leaning over.

"What do you know about your father, Naruto?" He asked tapping the manila folder under his hand with his index finger. "Do you know who he is?"

"You mean do I know that he is Tony Stark?" Naruto asked in return hoping he surprised the director but that man had a damn good poker face. "Or that he probably doesn't remember my mom? No, maybe it's, _'do I know'_ that Obidiah Stane paid my mother a ridiculous amount of money every year to keep me out of the spotlight because it would be bad for business?"

"You got pretty confident," The Directors' eye narrowed. "What happened to sir?"

"Yeah," Naruto shrugged. "Well, before I thought you guys were just gonna kill me. Put a bullet in my head then blow up my house and say it was a gas leak."

Now he knew that they wanted something from him. If he had to guess it would be something related to his father's technology. He didn't really care, the point was he had leverage.

Nick raised his eyebrow. "That's pretty morbid for a thirteen-year-old."

Naruto tensed. He didn't miss the fact that the director didn't bother denying that they would have killed him.

"Anyway," Nick stood up straight and flipped the folder open. "Father aside, Shield could use someone like you."

"Cool, talk to me in five years," Naruto said but still leaned over to get a better view of the picture inside.

 _"The Tesseract."_ Flipping through the photos, each taken at a different angle but always being centered around the glowing blue square. _"So SHIELD has had it all these years."_

He heard it went missing at the end of World War II. But of course, the government would have it hidden in one of their many black sites.

"We don't have that kind of time. Your country needs you now." Director Fury closed the folder. "It's either help us or spend the rest of your life in a hole. Make no mistake, kid. You're in a whole hell of a lot of trouble."

Naruto snorted. So it was either work for the government agency that kidnapped him and was now in the process of blackmailing him...or spend the rest of his life in a tiny cell. With the possibility of torture when he turned eighteen. Maybe before, he didn't know what kind of morals this Fury guy had.

"Guess we're partners then."

Director Fury smiled holding out his hand. "We're gonna do a lot of good things together, Mr. Uzumaki."

* * *

 **Naruto is the son of Tony Stark. He will have a variation of the Iron Man armor but that won't be all.**

 **Hope you guys like it!**


	2. Four Months

**Disclaimer: I Do Not** _O_ **wn Avengers Or Naruto**

* * *

 **Location, Unknown**

"What is this place?" Naruto asked as he was led into an old antique store by Agent Coulson who was in disguise. If you counted a Knicks hat and giants hoodie as a disguise.

Looking around the store he frowned at how fake the place looked. Hardwood floors, shelves of nick-knacks and antiquities. None of which were real.

"Okay, maybe some are real." Naruto would give SHIELD the benefit of the doubt but he knew for a fact the Jackson Pollock, convergence on the wall was a fake. His maternal grandmother had bought it sometime in the sixties and it was currently in the back of a storage container in California.

"Hello, nice weather we're having isn't it?" The clerk behind the checkout counter smiled.

She was an older lady, graying hair above her temples and lines on her face. If he had to guess Naruto would put her in the mid-forties. And really old fashioned.

 _"Who asks about the weather anymore?"_ He was actually almost positive he had never been asked about the weather. Ever. It was strange. Turning to Coulson to see how he reacted to the weird greeting his frown deepened.

"Yes, it's quite nice." Phil held the collapsible umbrella in his hand up. "But I always carry an umbrella just in case."

Naruto barely held the snort in his throat back. That sounded like a challenge code out of a spy movie.

"Follow me," Coulson ordered as the clerk's protective office split in half. Even the clerk split causing Naruto to flinch back in shock.

 _"What the hell?"_ Staring at the robot looking back at him with lifeless eyes he didn't even register the hand on his shoulder guiding him forward through the office still shocked by seeing a lifelike human split in half.

"She's a prototype. Only one in existence." Coulson explained as they entered an old-school elevator. With a gated door and fourteen yellow circle buttons.

Watching and memorizing each button his handler pressed Naruto looked away when Coulson glanced at him.

"The code changes daily."

"Okay," Naruto shrugged as the elevator jolted and began to lower.

"I know this probably isn't ideal for you but you will be helping a lot of people."

Rolling his eyes at the awkward attempt to console him Naruto leaned against the wall behind him, crossing his arms over his chest. "Are there new clothes wherever you are taking me?"

"Yes."

"Good, this prison suit is uncomfortable," Naruto opened his arms as if to showcase the grey baggy one-piece jumpsuit he was wearing. "I thought I was a consultant."

"You are. And you will be able to change once we arrive." Coulson said and just as he finished the elevator stopped. "Come on."

Following the agent out of the elevator as the gate door opened and the wall of the elevator shaft slid up.

"Whoa, you guys got all the toys, huh?" He joked his eyes moving around the room. **(Banners lab on Helicarrier)**

"Now you do too." Phil pressed a hand to the wall and the ground lit up holograms rising from the floor. "The room is one large holotable. Nothing like what Stark has but I'm sure you'll be able to make it work."

"Yeah, so what is my job exactly?" Moving around the room Naruto looked back at Agent Coulson who had stayed at the door. "The Director wasn't very forthcoming with the details."

"Whatever you want. Just know that everything you create will be SHIELD property and if the Director approves we'll use it. If you make a good impression, in a few months you won't even have to worry about a budget."

Naruto nodded but frowned. "Anything in particular?"

Having free reign to invent and build whatever he liked was cool but he needed some kind of direction. How else was he supposed to make a good impression and stay out of a black site if he didn't know what SHIELD wanted from him?

"Arc reactor technology."

Smiling Naruto tapped the table twice. That he could do. "Consider it done."

If Tony Stark could do it, so could he.

...

 **Stark Tower, Four months later**

"Tony!"

Staring at the hole in the wall of her office Pepper Potts flicked her eyes to the Iron man armor standing in the center of the room. "Why did you come through the wall? Do you know how much that is going to cost to fix?"

"You texted me." The Iron man helmet popped open revealing Tony Stark frowning at his girlfriend. "Come to the tower Asap. Followed by 911 and all capital EMERGENCY. I thought you were in danger."

" _We_ are in danger. But I need Tony Stark right now, not the Iron man." Pepper said with a glare trying not to look at the hole in her wall. It was only going to make her angry and right now that was _not_ what they needed.

Shifting as his armor moved around him opening like a cocoon, Tony stepped out smirking now that he knew Pepper wasn't in danger.

"So, you need me, huh?" He asked wiggling his hips provocatively. "I hope I can help."

" _That_ is not what I meant. Look at this," Pepper shoved a holotablet into Tony's chest. "Stark industries is no longer the only name in clean energy. We have a competitor and they just made ten billion dollars Tony. _Ten Billion_ , in one sale to the U.S government."

Flicking the tablet up Tony cocked his head at the news report that was hovering in the air. "Undisclosed contract? What is Wayne Enterprises building that's worth ten billion dollars?"

Weapons was the most obvious answer. What else would the U.S government pay billions of dollars for but neglect to share what they spent the money on with the general public?

"Some kind of gun maybe?" Tony frowned. His Iron man suits had repulsors that were powered by the Arc Reactor. Maybe instead of using it for flight Wayne Enterprises made weapons from it. And Assault rifle that could fire for hours without needing to be reloaded depending on the size. Or maybe a missile? A tank? Plane? All of the above?

"This isn't good," he muttered closing the hologram down.

He had gone to war with that idiotic senator to keep his technology out of the government's hands. It was too dangerous to let them have it. Yes, Rhodey was now the War Machine but he could shut that down whenever he wanted. The government just couldn't be trusted to use the Arc reactor technology without abusing it.

"Thank you. Now, that we're on the same page we need to talk contracts. Stark Industries needs to start putting our own Arc reactors on the market." Pepper said taking her tablet from Tony's hands. "How long will it take to mass produce them? Do you have blueprints we could send to the factories? We're playing catch up her Tony. We need to do something."

"I do have blueprints, yes. But, no, we won't be mass producing the Arc reactors. Not yet."

"Excuse me?" Pepper asked her eyes narrowing as Tony pulled the helmet off his armor and set it on his head. "Do you understand what is happening right now? Stark Industries doesn't have time for your games Tony. We thought we would be the only company in the world with this kind of Technology for years. Then that Russian showed up, and now Wayne Enterprises is selling their own design. Selling it Tony. Not making suits, making money. Our stocks are already dropping."

"Jarvis, find everything you can on Wayne Enterprises and forward it to my lab."

"Right away, sir."

"Tony! Are you listening?"

...

 **Location, Unknown**

"Congratulations, you're a billionaire." Slapping a folder down on Naruto's desk Fury crossed his arms a smirk on his face. "The World Security Council thanks Wayne Enterprises for their new Helicarrier."

Nodding Naruto ignored the folder and the director in favor of his work. Four months and not a single word from the director. Not a phone call, hell, not even a text. He recreated Starks new element, made Arc Reactors for SHIELD, and then used that technology to redesign the Helicarriers. And now the Director shows up telling him he's...a billionaire?

"Wait, what?" Grabbing the folder Naruto flipped it open skimming through the top three pages. "What the hell is Wayne Enterprises? I've never heard of it? Oh, and how the hell am I a billionaire!"

"No, need to shout." Fury said as he walked around the lab kicking the air up mattress on the floor into the corner. "You should really clean this place up."

Books were covering the desks, some closed and stacked together, and others were spread open. Around them, wrappers and containers of food were left out showcasing Naruto's diet of take out.

"This place is a mess."

"Well, I've been a little busy. You know arming SHIELD with the best technology available." Naruto held up a monthly report of Wayne Enterprises. "What is this?"

Maybe it was a little out of line to question the man who could have him killed if he wanted to but he wanted, no he needed answers. Being kept in the dark wasn't something he liked.

"Wayne Enterprises is the only company in the world selling clean energy. It's run by Minato Wayne, a half American and half Japanese man that will be dying in an unfortunate plane crash in a few years." Fury pointed at Naruto. "His son, Naruto Wayne will take over the family business and continue the good work his father did."

"My last name is Uzumaki. Not Wayne." Naruto slapped the folder shut. His name was how he was going to honor his mother. All the achievements, the good he was going to do for the world would have been under the name Uzumaki. It was why after she died he refused to contact his father. The Stark name would cast a shadow his mothers could never hope to escape.

Kushina Uzumaki's son would change the world. Not Tony Stark's.

Instead, he was in the dark. Creating things that _would_ change the world but not in the way he wanted. He wasn't making sure his mother's name would be remembered for the next hundreds of years. He was working in the shadows.

"If it was Uzumaki Enterprises, Tony Stark would recognize the name. He's already looking into the Wayne's." Fury leaned against the desk next to Naruto. "If he found out that you were Kushina Uzumaki's son he would look into you. And then he would find out your date of birth and put the pieces together. Having Tony Stark looking for his son would not be good for us."

"So I get a fake name and a fake company?"

"Oh, Wayne Enterprises is very real. All that money the World Security Council paid is very real. Like I said, you are now a billionaire. Not as rich as your father but give it a few years."

"Why?" Naruto frowned. He was working for SHIELD. Why would the director go through the trouble of creating a fake company that his organization would have to pay for the technology already in their hands? It didn't make sense.

Fury shook his head. "If the time comes you'll know."

"Do you try to be as cryptic as possible or does it come naturally?" Naruto asked as Fury moved away from the desk leaving the folder behind.

"Watch it, you're starting to sound like your father." Fury called over his shoulder as he walked back to the elevator. "Agent Coulson will be stopping by in a few days. He's gonna drop off some business books. If you're gonna run a company, you're going to need to know how."

The walls closed cutting off Naruto's view of the Director and locking him in his lab again. Turning his attention to the folder Fury left he scoffed and pushed it away. If SHIELD thought that making him a billionaire was going to gain his favor, then they were dead wrong. What was he going to do with a billion dollars? He was stuck in an underground lab.

No, Fury had to know that they couldn't keep him here forever and was taking measures to ensure that when he got out he wouldn't blow the whistle on SHIELD kidnapping a child.

 _"Well, it's not going to work."_ He thought going back to his work.

He was close. And being handed a company wasn't going to change his plan. Typing away at his computer he smirked. It would take a few years but he was getting out of this place. And SHIELD was going to hand deliver everything he needed to escape.

* * *

 **First few chapters will have quite a bit of time jumping. Writing Naruto being stuck in an underground lab, all alone, got repetitive so I'm cutting the _'filler'_.**

 **And hope you guys like the D.C Easter egg! Was going to make it Namikaze Enterprises but thought what the hell.**

 **Naruto will not be becoming Batman, just to avoid confusion. The names just to keep Tony from finding out he has a son.**

 **Anyway, hope you guys like it! Leave a review with what you think so far!**


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